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output_definition.json
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{
"files": {
"workflow-report": {
"filepath": "./wf-aav-qc-report.html",
"title": "Workflow report",
"description": "Report for all samples",
"mime-type": "text/html",
"optional": false,
"type": "aggregated"
},
"combined-reference": {
"filepath": "./combined_reference.fa.gz",
"title": "Combined reference sequence",
"description": "Reference file containing all AAV plasmid and host genome sequences.",
"mime-type": "application/gzip",
"optional": false,
"type": "aggregated"
},
"combined-reference-index": {
"filepath": "./combined_reference.fa.gz.fai",
"title": "Combined reference sequence index",
"description": "Index file for combined reference FASTA.",
"mime-type": "text/tab-separated-values",
"optional": false,
"type": "aggregated"
},
"compressed-combined-reference-index": {
"filepath": "./combined_reference.fa.gz.gzi",
"title": "Compressed combined reference sequence index",
"description": "Extra index file for combined reference FASTA (required because combined reference is bgzip-compressed).",
"mime-type": "application/octet-stream",
"optional": false,
"type": "aggregated"
},
"per-read-alignment-info": {
"filepath": "./{{ alias }}/{{ alias }}_bam_info.tsv",
"title": "Per read alignment info",
"description": "The result of `seqkit bam`.",
"mime-type": "text/tab-separated-values",
"optional": false,
"type": "per-sample"
},
"aav-structure-subtypes": {
"filepath": "./{{ alias }}/{{ alias }}_aav_per_read_info.tsv",
"title": "AAV structure assignment",
"description": "AAV per read genome subtypes.",
"mime-type": "text/tab-separated-values",
"optional": false,
"type": "per-sample"
},
"transgene_plasmid_consensus": {
"filepath": "./{{ alias }}/{{ alias }}_transgene_plasmid_consensus.fasta.gz",
"title": "Transgene plasmid consensus",
"description": "The transgene plasmid consensus sequence generated by medaka.",
"mime-type": "application/gzip",
"optional": false,
"type": "per-sample"
},
"transgene_plasmid_variants": {
"filepath": "./{{ alias }}/{{ alias }}_transgene_plasmid_variants.vcf.gz",
"title": "Transgene plasmid variants",
"description": "The transgene plasmid variants file generated by medaka.",
"mime-type": "application/gzip",
"optional": false,
"type": "per-sample"
},
"bam_all": {
"filepath": "./{{ alias }}/tagged_bams/sorted.tagged.bam",
"title": "Alignment file",
"description": "The resulting tagged BAM file from mapping reads to the combined reference.",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"bam_all_index": {
"filepath": "./{{ alias }}/tagged_bams/sorted.tagged.bam.bai",
"title": "Alignment index file",
"description": "The index for the resulting tagged BAM file from mapping reads to the combined reference.",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"bam_backbone_contamination": {
"filepath": "./{{ alias }}/tagged_bams/backbone_contamination.bam",
"title": "backbone_contamination alignment",
"description": "The resulting tagged BAM file from mapping reads to the combined reference. This file contains alignmnets with the genotype assignment: backbone_contamination",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"bam_index_backbone_contamination": {
"filepath": "./{{ alias }}/tagged_bams/backbone_contamination.bam.bai",
"title": "backbone_contamination alignment index",
"description": "The resulting tagged BAM index file from mapping reads to the combined reference. This indexes the file containing alignments with the genotype assignment: backbone_contamination",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"bam_full_ssaav": {
"filepath": "./{{ alias }}/tagged_bams/full_ssaav.bam",
"title": "full_ssaav alignment",
"description": "The resulting tagged BAM file from mapping reads to the combined reference. This file contains alignmnets with the genotype assignment: full_ssaav",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"bam_index_full_ssaav": {
"filepath": "./{{ alias }}/tagged_bams/full_ssaav.bam.bai",
"title": "full_ssaav alignment index",
"description": "The resulting tagged BAM index file from mapping reads to the combined reference. This indexes the file containing alignments with the genotype assignment: full_ssaav",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"bam_partial_ssaav": {
"filepath": "./{{ alias }}/tagged_bams/partial_ssaav.bam",
"title": "partial_ssaav alignment",
"description": "The resulting tagged BAM file from mapping reads to the combined reference. This file contains alignmnets with the genotype assignment: partial_ssaav",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"bam_index_partial_ssaav": {
"filepath": "./{{ alias }}/tagged_bams/partial_ssaav.bam.bai",
"title": "partial_ssaav alignment index",
"description": "The resulting tagged BAM index file from mapping reads to the combined reference. This indexes the file containing alignments with the genotype assignment: partial_ssaav",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"bam_full_scaav": {
"filepath": "./{{ alias }}/tagged_bams/full_scaav.bam",
"title": "full_scaav alignment",
"description": "The resulting tagged BAM file from mapping reads to the combined reference. This file contains alignmnets with the genotype assignment: full_scaav",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"bam_index_full_scaav": {
"filepath": "./{{ alias }}/tagged_bams/full_scaav.bam.bai",
"title": "full_scaav alignment index",
"description": "The resulting tagged BAM index file from mapping reads to the combined reference. This indexes the file containing alignments with the genotype assignment: full_scaav",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"bam_itr_region_only": {
"filepath": "./{{ alias }}/tagged_bams/itr_region_only.bam",
"title": "itr_region_only alignment",
"description": "The resulting tagged BAM file from mapping reads to the combined reference. This file contains alignmnets with the genotype assignment: itr_region_only",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"bam_index_itr_region_only": {
"filepath": "./{{ alias }}/tagged_bams/itr_region_only.bam.bai",
"title": "itr_region_only alignment index",
"description": "The resulting tagged BAM index file from mapping reads to the combined reference. This indexes the file containing alignments with the genotype assignment: itr_region_only",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"bam_complex": {
"filepath": "./{{ alias }}/tagged_bams/complex.bam",
"title": "complex alignment",
"description": "The resulting tagged BAM file from mapping reads to the combined reference. This file contains alignmnets with the genotype assignment: complex",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"bam_index_complex": {
"filepath": "./{{ alias }}/tagged_bams/complex.bam.bai",
"title": "complex alignment index",
"description": "The resulting tagged BAM index file from mapping reads to the combined reference. This indexes the file containing alignments with the genotype assignment: complex",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"bam_partial_scaav": {
"filepath": "./{{ alias }}/tagged_bams/partial_scaav.bam",
"title": "partial_scaav alignment",
"description": "The resulting tagged BAM file from mapping reads to the combined reference. This file contains alignmnets with the genotype assignment: partial_scaav",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"bam_index_partial_scaav": {
"filepath": "./{{ alias }}/tagged_bams/partial_scaav.bam.bai",
"title": "partial_scaav alignment index",
"description": "The resulting tagged BAM index file from mapping reads to the combined reference. This indexes the file containing alignments with the genotype assignment: partial_scaav",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"bam_unknown": {
"filepath": "./{{ alias }}/tagged_bams/unknown.bam",
"title": "unknown alignment",
"description": "The resulting tagged BAM file from mapping reads to the combined reference. This file contains alignmnets with the genotype assignment: unknown",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"bam_index_unknown": {
"filepath": "./{{ alias }}/tagged_bams/unknown.bam.bai",
"title": "unknown alignment index",
"description": "The resulting tagged BAM index file from mapping reads to the combined reference. This indexes the file containing alignments with the genotype assignment: unknown",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"igv-config": {
"filepath": "./igv.json",
"title": "IGV config JSON file",
"description": "JSON file with IGV config options to be used by the EPI2ME Desktop Application.",
"mime-type": "application/json",
"optional": false,
"type": "aggregated"
}
}
}